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Phaeodactylum tricornutum vs Guillardia theta CCMP2712 LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phaeodactylum tricornutum was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterPhaeodactylum tricornutumGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,331 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 26,204,989 out of 27,568,093
Covered: 1,363,104 out of 27,568,093

Uncovered: 16,576,115 out of 17,873,974
Matches: 787,696 out of 17,873,974
Mismatches: 463,492 out of 17,873,974
Insertions: 46,671 out of 17,873,974
Identity over aligned base-pairs: 60.7%

Guillardia theta CCMP2712

Uncovered: 85,784,846 out of 87,266,873
Covered: 1,482,027 out of 87,266,873

Uncovered: 29,311,816 out of 30,644,092
Matches: 806,289 out of 30,644,092
Mismatches: 475,638 out of 30,644,092
Insertions: 50,349 out of 30,644,092
Identity over aligned base-pairs: 60.5%

Block size distribution

Size range All 5,331 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
19
97.0 bp
10 bp - 100 bp
1,258
86.5 kb
226
16.1 kb
100 bp - 1 kb
3,739
1.3 Mb
1,747
794.7 kb
1 kb - 10 kb
314
448.9 kb
614
997.4 kb
10 kb - 100 kb
1
21.4 kb
1
21.4 kb